Hi everyone,
So I am familiar with using tophat for alignment and I used it successfully a few weeks ago with the following command:
tophat -p 4 –G ./Homo_sapiens.knownGene.hg19.sorted.withGenes.gtf --transcriptome-index=transcript_data/known hg19 ERR188021_1.fastq ERR188021_2.fastq &
When I previously ran this, it worked, however I ran it today with different fastq files and it gave me this error:
Error: Could not find Bowtie 2 index files (–G.*.bt2)
It seems like for some reason tophat thinks that -G is the base name for the index files instead of hg19. I have tried adding the full path for the hg19 but that gave the same error, I also tried getting rid of the --transcriptome-index part and that didn't change anything either. I need to have the -G reference transcript when running tophat but I don't know why this error is occuring. I tried to recreate the index files from bowtie2-build and put all 6 files into a folder titled Index which was located on my desktop and then in the above command, changed hg19 to /Path/Desktop/Index/hg19. This also failed as well.
This is really frustrating because the same exact command was working just a few weeks ago. I have top hat version 2.0.11 and bowtie2 version 2.2.3
I really need some help on this since I spent many hours trying to solve this problem. Any help would GREATLY be appreciated.
THANK YOU!!!
So I am familiar with using tophat for alignment and I used it successfully a few weeks ago with the following command:
tophat -p 4 –G ./Homo_sapiens.knownGene.hg19.sorted.withGenes.gtf --transcriptome-index=transcript_data/known hg19 ERR188021_1.fastq ERR188021_2.fastq &
When I previously ran this, it worked, however I ran it today with different fastq files and it gave me this error:
Error: Could not find Bowtie 2 index files (–G.*.bt2)
It seems like for some reason tophat thinks that -G is the base name for the index files instead of hg19. I have tried adding the full path for the hg19 but that gave the same error, I also tried getting rid of the --transcriptome-index part and that didn't change anything either. I need to have the -G reference transcript when running tophat but I don't know why this error is occuring. I tried to recreate the index files from bowtie2-build and put all 6 files into a folder titled Index which was located on my desktop and then in the above command, changed hg19 to /Path/Desktop/Index/hg19. This also failed as well.
This is really frustrating because the same exact command was working just a few weeks ago. I have top hat version 2.0.11 and bowtie2 version 2.2.3
I really need some help on this since I spent many hours trying to solve this problem. Any help would GREATLY be appreciated.
THANK YOU!!!
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